Contacts of the helix formed by residues 2395 - 2405 (chain B) in PDB entry 2H7C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU2395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2391B ILE* 3.9 11.9 - - + -
2392B ALA* 2.9 25.5 + - + +
2394B GLU* 1.3 99.7 - - + +
2396B ILE* 1.3 63.6 + - - +
2397B PRO* 3.4 2.9 - - - -
2398B GLU* 3.4 26.7 + - - +
2399B ALA* 3.2 21.3 + - - +
2550B LEU* 3.5 40.5 - - + +
2551B PHE* 5.0 8.7 - - + -
2553B LYS* 4.1 25.4 - - + +
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Residues in contact with ILE2396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2379B MET* 3.6 44.4 - - + +
2382B LEU* 3.9 28.9 - - + +
2383B TRP* 4.3 6.7 - - + +
2391B ILE* 3.3 38.8 - - + +
2392B ALA 3.3 4.0 + - - +
2393B LYS* 3.4 24.7 - - + +
2395B LEU* 1.3 77.9 - - - +
2397B PRO* 1.3 72.3 - - + +
2399B ALA* 3.3 2.1 + - - +
2400B THR* 2.9 30.8 + - - +
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Residues in contact with PRO2397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2379B MET* 4.0 25.1 - - - -
2393B LYS 3.6 9.9 - - - +
2394B GLU* 3.8 9.4 - - - +
2395B LEU 3.5 3.4 - - - -
2396B ILE* 1.3 95.1 - - + +
2398B GLU* 1.3 60.5 + - + +
2400B THR* 3.7 1.2 - - - -
2401B GLU* 2.8 32.6 + - - +
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Residues in contact with GLU2398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2394B GLU 4.3 7.3 - - - +
2395B LEU* 3.4 23.5 + - - +
2396B ILE 3.3 0.6 - - - -
2397B PRO* 1.3 76.4 - - + +
2399B ALA* 1.3 65.2 + - - +
2401B GLU* 3.9 4.1 - - - +
2402B LYS* 2.8 27.7 + - - +
2546B PHE* 4.4 5.7 - - + -
2550B LEU* 3.0 22.0 - - + +
2553B LYS* 2.6 33.8 + - - +
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Residues in contact with ALA2399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2382B LEU* 4.2 15.0 - - + -
2391B ILE* 4.6 3.6 - - + -
2395B LEU 3.2 10.4 + - - +
2396B ILE* 3.6 7.0 - - - +
2398B GLU* 1.3 79.0 - - - +
2400B THR* 1.3 62.6 + - - +
2402B LYS* 3.5 2.9 + - - +
2403B TYR* 3.3 26.5 + - - -
2420B LEU* 3.9 4.0 - - + +
2546B PHE* 3.9 12.8 - - - -
2547B TRP* 3.8 26.5 - - + -
2550B LEU* 3.8 8.0 - - + +
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Residues in contact with THR2400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2375B GLN* 4.2 18.4 - - + +
2378B ALA* 4.0 26.4 - - + -
2379B MET* 3.7 26.4 - - + +
2382B LEU* 3.7 14.9 - - - +
2396B ILE* 2.9 18.5 + - - +
2397B PRO* 3.7 2.7 - - - -
2399B ALA* 1.3 74.5 - - - +
2401B GLU* 1.3 60.6 + - - +
2403B TYR 3.3 0.9 + - - -
2404B LEU* 2.8 38.0 + - + +
2417B PHE* 5.6 1.9 - - + -
2420B LEU* 4.6 7.5 - - - +
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Residues in contact with GLU2401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2375B GLN* 2.9 29.0 + - - +
2397B PRO 2.8 21.1 + - - +
2398B GLU* 3.9 4.5 - - - +
2400B THR* 1.3 73.0 - - - +
2402B LYS* 1.3 60.3 + - - +
2405B GLY* 2.7 55.3 + - - +
2406B GLY 4.4 0.2 + - - -
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Residues in contact with LYS2402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2398B GLU 2.8 18.0 + - - +
2399B ALA 3.5 3.1 - - - +
2400B THR 3.2 0.2 - - - -
2401B GLU* 1.3 78.9 - - - +
2403B TYR* 1.3 66.1 + - + +
2405B GLY 4.8 0.3 + - - -
2406B GLY 5.4 1.6 + - - -
2542B LYS 5.9 0.7 - - - -
2546B PHE* 3.4 57.9 - - + +
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Residues in contact with TYR2403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2399B ALA 3.3 16.2 + - - +
2400B THR 3.3 2.9 + - - +
2402B LYS* 1.3 89.4 - - + +
2404B LEU* 1.3 63.4 + - + +
2406B GLY 4.8 2.4 + - - -
2416B LEU* 3.1 52.0 - - + +
2419B ASP* 4.2 6.7 - - + -
2420B LEU* 3.6 32.1 - - + -
2423B ASP* 2.6 31.0 + - - -
2543B GLU* 3.5 13.8 - - + +
2546B PHE* 4.2 10.1 - + - -
2547B TRP* 2.9 40.0 + + - -
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Residues in contact with LEU2404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2373B LEU* 4.8 2.7 - - + +
2375B GLN* 3.5 16.6 - - + +
2378B ALA* 3.8 29.2 - - + -
2400B THR* 2.8 27.0 + - + +
2403B TYR* 1.3 76.7 - - + +
2405B GLY* 1.3 52.7 + - - +
2406B GLY 3.0 11.1 + - - -
2407B THR* 3.2 8.3 + - - +
2413B LYS* 2.7 73.0 + - + +
2416B LEU* 3.4 23.3 - - + -
2417B PHE* 3.5 17.5 - - + +
2420B LEU* 5.9 0.7 - - + -
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Residues in contact with GLY2405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2375B GLN* 3.3 12.9 + - - -
2401B GLU* 2.7 49.5 + - - +
2404B LEU* 1.3 70.9 - - - +
2406B GLY* 1.3 57.0 + - - +
2407B THR 3.3 3.5 + - - -
2413B LYS* 4.3 1.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il